Build - Sep 2024 files

[twhetzel]

Resolves #ISSUE(s).

Overview

This PR:

• Full build files for September Lexical Alignment review
  NOTE: No new changes from develop are included in main for this PR for this month's build to create lexical alignment files.

Pre-merge checklist

Documentation

Was the documentation added/updated under docs/?

• Yes
• No, updates to the docs were not necessary after careful consideration

QC

Was the full pipeline run before submitting this PR using sh run.sh make build-mondo-ingest on this branch (after
docker pull obolibrary/odkfull:dev), and no errors occurred?

• Yes
• No, there are no functional (code-related) changes to the pipeline in the PR, so no re-run is necessary

New Packages

Were any new Python packages added?

• Yes, requirements.txt.full was updated and an ODK issue submitted
• No

Were any other non-Python packages added?

• Yes, Dockerfile updated and an ODK issue submitted
• No

PR Review and Conversations Resolved

Has the PR been sufficiently reviewed by at least 1 team member of the Mondo Technical team and all threads resolved?

• Yes

[joeflack4]

LGTM.

Just some observations of some things that changed more than others, but all seems normal to me.

• DOID: Plenty new in lexmatch, mapping status, 60~ new in component signature.
• Orphanet: 80 new in ordo-subsets.robot.tsv, 70 less entries in unmapped. Most entries in mondo_closematch_orphanet.tsv gone now (this one, I'm not really sure why).
• unmapped_icd11foundation_lex_exact.tsv: Previously empty; now has rows!
• OMIM: lexmatch, I see label changes, and many new match entries to NCBI or HGNC genes. This correspond to component_signature-omim.tsv, with 3.5k more lines, almost completely due to new HGNC entries. Expected / fair amount of new entries to mapping status and slurp.